miRNA: 3'- -CUGUaGCGAUCGC---AUGA----------CAGCGCGUu -5'
miRNA: 3'- -CUGUAGCGAUCGCAUgA-CAGCgcguu -5'
miRNA: 3'- -CUGUAGCGAUC-GCaUGAC-AGC-GCGuu -5'
miRNA: 3'- -CUGua--GCGAUCGCa--UGACAGCG----CGUU- -5'
miRNA: 3'- -CUGUAGCGAUCGCAUGACAGCGCGUU- -5'
Results 1 - 5 of 5 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. | strand | Start Position | R_P_ratio# |
P value
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| Predicted miRNA align pattern | |||||||
| 8788 | 5' | -53.7 | NC_002484.1 | + | 8207 | 0.66 | 0.747915 |
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Target: 5'- aGGCAgCGCUGGCGaugUACUcaggcaguggGUUGCGCGu -3' miRNA: 3'- -CUGUaGCGAUCGC---AUGA----------CAGCGCGUu -5' |
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| 8788 | 5' | -53.7 | NC_002484.1 | + | 19814 | 0.66 | 0.737173 |
|
Target: 5'- uGACAUCGCUAGCGUAgUaGUUGg---- -3' miRNA: 3'- -CUGUAGCGAUCGCAUgA-CAGCgcguu -5' |
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| 8788 | 5' | -53.7 | NC_002484.1 | + | 41695 | 0.67 | 0.670807 |
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Target: 5'- aGAUAUCGCUGGcCGaGCUGcUCGcCGCc- -3' miRNA: 3'- -CUGUAGCGAUC-GCaUGAC-AGC-GCGuu -5' |
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| 8788 | 5' | -53.7 | NC_002484.1 | + | 41748 | 0.68 | 0.659541 |
|
Target: 5'- cGACcgcgCGCUGGCGaugGCUGUUGCugacGCAGg -3' miRNA: 3'- -CUGua--GCGAUCGCa--UGACAGCG----CGUU- -5' |
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| 8788 | 5' | -53.7 | NC_002484.1 | + | 517 | 1.06 | 0.001851 |
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Target: 5'- cGACAUCGCUAGCGUACUGUCGCGCAAu -3' miRNA: 3'- -CUGUAGCGAUCGCAUGACAGCGCGUU- -5' |
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Note:
When operating RNAhybrid, the pipeline first calculates the perfect minimum free energy (Perfect mfe *) of a putative miRNA when the entire putative miRNA binds to a perfectly complementary target site, then it calculates the minimum free energy of RNA duplex (mfe of the miRNA/mRNA duplex), abbreviated as Rd_mfe. An alignment for which the Rd_mfe to its correspondent Perfect mfe ratio (R_P_ratio #) is more than 66% is regarded as a positive alignment as described by Krek et al. (21). The P_value is calculated by RNAhybrid.
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